[2023-06-28 12:34:07,594] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:34:07,598] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:34:07,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference
[2023-06-28 12:34:09,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:34:09,060] [INFO] Task started: Prodigal
[2023-06-28 12:34:09,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg680e82b0-32b6-4f1b-bb7c-73fca1df50b1/GCA_017694995.1_ASM1769499v1_genomic.fna.gz | prodigal -d GCA_017694995.1_ASM1769499v1_genomic.fna/cds.fna -a GCA_017694995.1_ASM1769499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:34:21,873] [INFO] Task succeeded: Prodigal
[2023-06-28 12:34:21,874] [INFO] Task started: HMMsearch
[2023-06-28 12:34:21,874] [INFO] Running command: hmmsearch --tblout GCA_017694995.1_ASM1769499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference/reference_markers.hmm GCA_017694995.1_ASM1769499v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:34:22,132] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:34:22,133] [INFO] Found 6/6 markers.
[2023-06-28 12:34:22,157] [INFO] Query marker FASTA was written to GCA_017694995.1_ASM1769499v1_genomic.fna/markers.fasta
[2023-06-28 12:34:22,157] [INFO] Task started: Blastn
[2023-06-28 12:34:22,158] [INFO] Running command: blastn -query GCA_017694995.1_ASM1769499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference/reference_markers.fasta -out GCA_017694995.1_ASM1769499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:22,775] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:22,780] [INFO] Selected 29 target genomes.
[2023-06-28 12:34:22,780] [INFO] Target genome list was writen to GCA_017694995.1_ASM1769499v1_genomic.fna/target_genomes.txt
[2023-06-28 12:34:22,783] [INFO] Task started: fastANI
[2023-06-28 12:34:22,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg680e82b0-32b6-4f1b-bb7c-73fca1df50b1/GCA_017694995.1_ASM1769499v1_genomic.fna.gz --refList GCA_017694995.1_ASM1769499v1_genomic.fna/target_genomes.txt --output GCA_017694995.1_ASM1769499v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:34:40,206] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:40,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:34:40,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:34:40,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:34:40,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:34:40,212] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-28 12:34:40,215] [INFO] DFAST Taxonomy check result was written to GCA_017694995.1_ASM1769499v1_genomic.fna/tc_result.tsv
[2023-06-28 12:34:40,216] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:34:40,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:34:40,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference/checkm_data
[2023-06-28 12:34:40,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:34:40,254] [INFO] Task started: CheckM
[2023-06-28 12:34:40,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017694995.1_ASM1769499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017694995.1_ASM1769499v1_genomic.fna/checkm_input GCA_017694995.1_ASM1769499v1_genomic.fna/checkm_result
[2023-06-28 12:35:19,902] [INFO] Task succeeded: CheckM
[2023-06-28 12:35:19,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.68%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:35:19,928] [INFO] ===== Completeness check finished =====
[2023-06-28 12:35:19,929] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:35:19,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017694995.1_ASM1769499v1_genomic.fna/markers.fasta)
[2023-06-28 12:35:19,929] [INFO] Task started: Blastn
[2023-06-28 12:35:19,929] [INFO] Running command: blastn -query GCA_017694995.1_ASM1769499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e5ea7c-ca3f-4a50-a201-83fd3e77489d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017694995.1_ASM1769499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:35:20,717] [INFO] Task succeeded: Blastn
[2023-06-28 12:35:20,721] [INFO] Selected 17 target genomes.
[2023-06-28 12:35:20,721] [INFO] Target genome list was writen to GCA_017694995.1_ASM1769499v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:35:20,722] [INFO] Task started: fastANI
[2023-06-28 12:35:20,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg680e82b0-32b6-4f1b-bb7c-73fca1df50b1/GCA_017694995.1_ASM1769499v1_genomic.fna.gz --refList GCA_017694995.1_ASM1769499v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017694995.1_ASM1769499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:35:28,263] [INFO] Task succeeded: fastANI
[2023-06-28 12:35:28,277] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:35:28,277] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_017694995.1	s__Cryptobacteroides faecavium	100.0	700	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017695065.1	s__Cryptobacteroides excrementipullorum	84.1675	398	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695115.1	s__Cryptobacteroides avicola	80.1952	309	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694885.1	s__Cryptobacteroides faecipullorum	79.3108	288	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760425.1	s__Cryptobacteroides sp900760425	77.8967	124	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694845.1	s__Cryptobacteroides intestinavium	77.6446	118	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694835.1	s__Cryptobacteroides gallistercoris	77.5401	128	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694755.1	s__Cryptobacteroides merdavium	77.5009	175	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694785.1	s__Cryptobacteroides intestinigallinarum	77.4264	150	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694655.1	s__Cryptobacteroides merdigallinarum	77.0759	147	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017695025.1	s__Cryptobacteroides excrementavium	77.0137	135	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631875.1	s__Cryptobacteroides sp017631875	76.5847	59	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399865.1	s__Cryptobacteroides sp017399865	76.2261	68	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461285.1	s__Cryptobacteroides sp017461285	76.0531	80	706	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:35:28,280] [INFO] GTDB search result was written to GCA_017694995.1_ASM1769499v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:35:28,280] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:35:28,283] [INFO] DFAST_QC result json was written to GCA_017694995.1_ASM1769499v1_genomic.fna/dqc_result.json
[2023-06-28 12:35:28,283] [INFO] DFAST_QC completed!
[2023-06-28 12:35:28,283] [INFO] Total running time: 0h1m21s